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Crystal structure determination of Catechol 1,2-Dioxygenase from Rhodococcus opacus 1CP in complex with 3,5-dichlorocatechol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 296 PEG 400 38%, MGCL2 0.1 M, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.14 42.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.818 α = 90 b = 37.619 β = 94.81 c = 74.817 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2007-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 1.0028 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.85 74.7 96.8 0.05 0.05 15.2 3.6 21143 21143 31.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.85 1.95 93.4 0.539 0.539 2.2 3.4 2943
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3HGI 1.85 74.54 20060 1081 96.75 0.20705 0.20384 0.2035 0.26712 0.2644 RANDOM 34.908
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.81 0.02 0.61 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.888 r_dihedral_angle_4_deg 23.997 r_dihedral_angle_3_deg 16.968 r_dihedral_angle_1_deg 6.506 r_scangle_it 3.584 r_scbond_it 2.458 r_angle_refined_deg 1.728 r_mcangle_it 1.695 r_mcbond_it 1.057 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.888 r_dihedral_angle_4_deg 23.997 r_dihedral_angle_3_deg 16.968 r_dihedral_angle_1_deg 6.506 r_scangle_it 3.584 r_scbond_it 2.458 r_angle_refined_deg 1.728 r_mcangle_it 1.695 r_mcbond_it 1.057 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.289 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.238 r_symmetry_hbond_refined 0.208 r_chiral_restr 0.142 r_metal_ion_refined 0.096 r_bond_refined_d 0.018 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2002 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 52
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling